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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Evolutionary Transitions Drive Molecular Adaptation in Sculpin Rhodopsin
Esmé S B Macpherson1,2, Belinda S W Chang2,3, Nathan R Lovejoy4,5,6
1Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
Journal of Molecular Evolution
|July 11, 2026
Summary
Sculpin fish rhodopsin genes show rapid evolution driven by habitat changes. Freshwater transitions shift vision towards red light, while deep-water adaptation shifts it towards blue light.
Area of Science:
- Evolutionary biology
- Genomics
- Sensory systems evolution
Background:
- Habitat transitions in fishes, particularly between marine and freshwater, drive rapid adaptation in sensory systems.
- The visual system is particularly sensitive to changes in aquatic environments, leading to evolutionary divergence at all levels.
- Sculpins (Cottoidea) are a diverse fish group inhabiting various benthic environments, making them ideal for studying visual system evolution.
Purpose of the Study:
- To investigate the evolutionary trajectory of dim light-sensitive rhodopsin genes in sculpins.
- To understand how habitat transitions, including marine-freshwater shifts and deep-sea adaptation, have influenced rhodopsin evolution and function.
- To identify selective pressures and functional adaptations in sculpin rhodopsin genes across diverse habitats.
Main Methods:
- Employed molecular evolution models to analyze selective pressures on cottoid rhodopsin genes.
- Estimated spectral absorbance of rhodopsin proteins across various sculpin species.
- Compared rhodopsin evolution in marine (Psychrolutidae) and freshwater (Cottidae) sculpins, including endemic Lake Baikal species.
Main Results:
- Pervasive positive selection was detected across sculpin rhodopsin genes.
- Freshwater transition and radiation led to genetic diversification and a red-shifted spectral absorbance.
- Lake Baikal sculpins adapted to deep waters by progressively blue-shifting rhodopsin.
- Marine Psychrolutidae rhodopsins are under strong positive selection, with spectral absorbance potentially linked to non-spectral adaptations for dim-light vision and migratory life history.
Conclusions:
- Habitat transitions are significant drivers of functional diversity in sculpin rhodopsin genes.
- Sculpin visual systems exhibit remarkable adaptation to diverse light environments, from shallow freshwater to the deep sea.
- Rhodopsin evolution in sculpins highlights the interplay between environmental pressures, genetic adaptation, and sensory system function.
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